| Round of 16 — Direct Qualification | ||||||||||
| 1 | Lyon | 8 | 8 | 0 | 0 | 31 | 4 | +27 | 24 | Direct |
| 2 | Monaco | 8 | 7 | 1 | 0 | 33 | 6 | +27 | 22 | Direct |
| 3 | Basel | 8 | 7 | 1 | 0 | 26 | 10 | +16 | 22 | Direct |
| 4 | Tottenham | 8 | 6 | 1 | 1 | 22 | 7 | +15 | 19 | Direct |
| 5 | Rennes | 8 | 6 | 1 | 1 | 18 | 7 | +11 | 19 | Direct |
| 6 | Villarreal | 8 | 6 | 0 | 2 | 19 | 10 | +9 | 18 | Direct |
| 7 | Midtjylland | 8 | 6 | 0 | 2 | 15 | 11 | +4 | 18 | Direct |
| 8 | Augsburg | 8 | 5 | 2 | 1 | 23 | 6 | +17 | 17 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Rapid Wien 2 | 8 | 5 | 2 | 1 | 16 | 13 | +3 | 17 | Playoff |
| 10 | Valencia | 8 | 5 | 1 | 2 | 20 | 10 | +10 | 16 | Playoff |
| 11 | AZ Alkmaar | 8 | 4 | 3 | 1 | 18 | 18 | 0 | 15 | Playoff |
| 12 | Genk | 8 | 4 | 1 | 3 | 14 | 12 | +2 | 13 | Playoff |
| 13 | Vikingur Reykjavik | 8 | 4 | 1 | 3 | 12 | 12 | 0 | 13 | Playoff |
| 14 | Braga | 8 | 3 | 2 | 3 | 14 | 12 | +2 | 11 | Playoff |
| 15 | Rapid Wien | 8 | 3 | 2 | 3 | 14 | 14 | 0 | 11 | Playoff |
| 16 | Manchester United | 8 | 3 | 2 | 3 | 13 | 14 | -1 | 11 | Playoff |
| 17 | Glentoran | 8 | 3 | 1 | 4 | 15 | 14 | +1 | 10 | Playoff |
| 18 | Elbasani | 8 | 2 | 3 | 3 | 14 | 15 | -1 | 9 | Playoff |
| 19 | Red Star | 8 | 2 | 3 | 3 | 12 | 13 | -1 | 9 | Playoff |
| 20 | Ajax 2 | 8 | 2 | 3 | 3 | 8 | 9 | -1 | 9 | Playoff |
| 21 | LASK | 8 | 2 | 3 | 3 | 12 | 16 | -4 | 9 | Playoff |
| 22 | Europa FC | 8 | 2 | 3 | 3 | 16 | 21 | -5 | 9 | Playoff |
| 23 | Club Brugge 2 | 8 | 2 | 3 | 3 | 15 | 21 | -6 | 9 | Playoff |
| 24 | Vitesse | 8 | 3 | 0 | 5 | 14 | 21 | -7 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | AS Roma | 8 | 3 | 0 | 5 | 11 | 19 | -8 | 9 | Out |
| 26 | Eintracht Frankfurt | 8 | 2 | 2 | 4 | 13 | 25 | -12 | 8 | Out |
| 27 | Ludogorets | 8 | 1 | 4 | 3 | 11 | 14 | -3 | 7 | Out |
| 28 | Slavia Prague | 8 | 2 | 1 | 5 | 10 | 16 | -6 | 7 | Out |
| 29 | Real Betis | 8 | 1 | 3 | 4 | 10 | 13 | -3 | 6 | Out |
| 30 | Hearts | 8 | 1 | 3 | 4 | 8 | 16 | -8 | 6 | Out |
| 31 | Slavia Prague 2 | 8 | 1 | 3 | 4 | 13 | 23 | -10 | 6 | Out |
| 32 | Ordabasy | 8 | 1 | 1 | 6 | 18 | 24 | -6 | 4 | Out |
| 33 | Twente | 8 | 1 | 1 | 6 | 13 | 25 | -12 | 4 | Out |
| 34 | Lincoln Red Imps | 8 | 1 | 1 | 6 | 7 | 19 | -12 | 4 | Out |
| 35 | Sparta Prague 2 | 8 | 1 | 0 | 7 | 8 | 28 | -20 | 3 | Out |
| 36 | Hibernians | 8 | 0 | 0 | 8 | 7 | 25 | -18 | 0 | Out |